In all likelihood, you just need to shim your focus screen, or someone replaced the focus screen and did not re ck the focus afterwards. If the focus screen was replaced w/ a non Minolta screen w/o a fresnel, you may have to adjust things to get it right. The standard Autocord screen has a large circle in the center that is used to give you an easier focus area to see when you focus. Someone also could have replaced the mirror and not gotten it locked down all the way. I know what you mean about the camera being difficult to hold w/ the back door open and a ground glass on the film rails. You can tape the GG to the film rails, and just balance the camera on the tripod as best you can. It works well enough this way to get a focus ck on the GG on the film rails w/ a loupe.
Simply pull the 4 screws out that hold the top hood on, carefully pull the hood up and off, and ck to see if the mirror's 2 screws are tight and the mirror is lying flat. If someone replaced the mirror w/ one that is a different thickness, that's your problem. Ck to see if the focus screen has a fresnel under the focus screen (if it has the stock Minolta focus screen installed). It should be on the bottom of the camera's focus screen. If everything looks OK, put the back on the camera, lock the camera down on the tripod, place the focus on infinity, put the top hood back on w/o the screws, unfold the magnifying glass, and carefully pull the hood up a little and see if the image gets sharper on the focus screen. If it does, place 2 little shims of cut paper cards (playing cards work great) on either side of the top hood on the bottom, place the hood back on the camera, hold it down snug, and see how the focus now looks. Keep shimming and checking as needed until you get a sharp image, then lock it down w/ the 4 screws (they don't have to be snugged down too tightly) and reconfirm that the image on the focus screen is sharp at infinity. Since you already confirmed that the taking lens is properly focused at infinity, you're now done.
Nearly every time you have a focus issue on a TLR it's related to the focus screen or mirror. Unless the camera has been dropped and the lens board is visibly bent, it's doubtful the two lenses are out of sync.